|
| Status |
Public on Oct 09, 2017 |
| Title |
N2_Sba_8 |
| Sample type |
SRA |
| |
|
| Source name |
L1 larvae
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
buffer: S-basal
developmental stage: L1 larvae
|
| Treatment protocol |
Embryos were grown in S-basal (with or without 50mM trehalose) at a density of 1 embryo/uL. After 24 hours, L1 larvae were spun down and flash frozen in liquid nitrogen and stored at -80C until RNA extraction.
|
| Growth protocol |
Strains were grown on OP50 plates at 20C, and adults were hypochlorite treated to obtain embryos.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol with minor modifications to the manufacturer's protocol. 1mL of TRIzol was used per sample. Samples were homogenized using 100uL of acid-washed sand.
Libraries were prepared using the NEB Next Ultra Non-directional mRNA-seq Kit. 500ng of starting RNA was used and 12 cycles of PCR were used to amplify libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Bowtie version 1.1.2 was used to map reads to the WS210 version of the genome.
Count files were generated with HTSeq using the GTF file used in Maxwell et al., 2012. This file includes features of the WS210 genome in addition to features of WS220 mapped back to WS210.
edgeR exact test was used on normalized count tables for differential expression analysis. Genes with counts per million (CPM) >1 in at least 4 libraries were included in the analysis.
Genome_build: WS210
Supplementary_files_format_and_content: Count files include the sequence identifier for each gene and the number of counts mapping to that gene (not normalized across libraries).
|
| |
|
| Submission date |
May 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Amy K Webster |
| E-mail(s) |
awebst10@uoregon.edu
|
| Organization name |
University of Oregon
|
| Street address |
Institute of Ecology and Evolution
|
| City |
Eugene |
| State/province |
Oregon |
| ZIP/Postal code |
97703 |
| Country |
USA |
| |
|
| Platform ID |
GPL22765 |
| Series (1) |
| GSE98544 |
mRNA-seq comparison of N2 and tps1;tps2 double mutants with and without trehalose supplementation |
|
| Relations |
| BioSample |
SAMN06890675 |
| SRA |
SRX2783748 |
